This application addresses Broad Challenge Area (08) Genomics and Specific Challenge Topic 08-AG-106 Cross-disease research to identify commonly targeted pathways or mechanisms between low incidence, neurogenetic disorders with high incidence, population-based disease. The goal of this proposal is to identify novel genes that are responsible for mendelian, highly penetrant familial dementia (FD) of either Alzheimer's disease (AD) or frontotemporal dementia (FTD) subtype. This will be accomplished by sequencing the whole genome protein-coding portion ("exome") in a collection of 10 families with FD that were ascertained, phenotyped and sampled over a period of 30 years at the University of Washington Alzheimer's Disease Research Center (ADRC). The extensive ADRC collection is a valuable resource for the discovery of new genes responsible for cognitive decline and neurodegeneration. The identification of FD genes and associated mutations will facilitate discovery of additional causal genes in several ways. First, analysis of newly uncovered or broadened biological pathways will bring to light new dementia candidate genes for more targeted studies. Second, the genetic heterogeneity of FD of unknown cause will be diminished as families are assigned to subgroups on the basis of mutations in newly found FD genes. Third, these genes, in turn, will implicate additional pathways involved and will increase the number of targets for therapeutic interventions. Finally, to benefit the scientific and clinical communities at large and to facilitate corroboration of our findings in other samples, we will deposit FD genotype and phenotype information into the on-line resources GeneTests and the NCBI Variation Databases (dbSNP and dbGaP). In the past two decades genetic studies and positional cloning in families have identified genes for numerous mendelian diseases. Researchers from the ADRC have been in the forefront of this effort and have had a major role in discovery of multiple genes, including PSEN1, PSEN2 and MAPT. This important work currently allows for accurate diagnosis of monogenic dementias, expands our understanding of the biology of neurodegeneration and has laid the foundations for new treatments that might be applicable for common FDs with complex etiology. However for many affected families the causal genes have not yet been found. Many of these families are too small for positional cloning. Previously there were no methods for identification of novel causative genes when DNA from only a few affected persons was available, despite an extensive family history of disease. In this proposal we will capitalize on newly available massively parallel sequencing coupled with advances in genome annotation and bioinformatics to apply mutational cloning of the exome as a powerful and innovative approach for identification of genes involved in FD. Mutational cloning is based on the concept of exclusion mapping. Within a family, all affected individuals must share the mutation responsible for the disease, and all nonshared variants are excluded. From the genomes of already sequenced individuals we estimate that each individual bears approximately 10,000 protein-changing alterations. Because mutations responsible for autosomal dominant forms of FD must be rare they are not likely to be present in dbSNP with a stated frequency. Approximately 90 percent of protein- changing variants are present in dbSNP at this time. This leaves an average of 1000 unique variants for each sequenced individual. This number is an overestimate, as with further increases in resequencing (e.g., the 1000 Genomes Project), the number of less common variants in dbSNP will grow. Current experience with over 2000 cloned mendelian genes strongly supports the contention that disease causing mutations affect highly conserved residues. Some variants will predict conservative amino acid substitutions unlikely to damage the protein. We estimate that 80% of unique variants can be eliminated based on these tenets. With these criteria, approximately 200 candidate variants will remain for each exome, quite similar to the number of genes contained in the minimal linkage region from a positional cloning approach. The exome of the second affected person in the family will exclude a portion of these variants from further consideration. Because sibs share on average 50% of the genome, an affected sib pair has the potential to reduce the number of candidate mutations by half. With even slightly expanded families this number will diminish more dramatically. Cousins share on average 12.5% of the genome and can reduce the number of candidate mutations from 200 to 25. Failure of the variant to cosegregate with disease in the other affected people in the family will eliminate yet more variants. The remaining candidate genes will be prioritized for studies in additional families and dementia cases on the basis of gene function, tissue expression, conservation, predicted effect of the mutation, existence of animal models, involvement in human diseases, and other cues from the literature. We are poised to take maximal advantage of the confluence of infrastructure (University of Washington Department of Genome Sciences), expertise in molecular genetics (Drs. Raskind, Shendure, and Brkanac), existing well- characterized samples (Dr. Bird), and advances in sequencing techniques that now make it feasible to do whole exome screening without preconceived candidate genes. PUBLIC HEALTH RELEVANCE: The goal of this proposal is to identify novel genes that are responsible for mendelian, highly penetrant familial dementia (FD) of either Alzheimer's disease (AD) or frontotemporal dementia (FTD) subtype. We will employ newly available powerful sequencing and bioinformatics techniques to detect causative mutations in families with apparent autosomal dominant dementia where the available affected persons are too few for linkage analyses.